We examined associations between riparian canopy cover, presence or absence of cattle, rainfall, solar radiation, month of year, dissolved oxygen, turbidity, salinity, and Enterococcus concentrations in riparian surface soils with Enterococcus geometric mean in-stream water concentrations at Waipā watershed on the north side of the Hawaiian island Kaua'i. Each 1% decrease in riparian canopy cover was associated with a 4.6 most probable number (MPN)/100 ml increase of the geometric mean of Enterococcus in stream water (P < 0.05). Each unit decrease in salinity (ppt) was associated with an increase of Enterococcus by 68.2 MPN/100 ml in-stream water geometric mean concentrations (P < 0.05). Month of year was also associated with increases in stream water Enterococcus geometric mean concentrations (P < 0.05). Reducing riparian canopy cover is associated with Enterococcus increases in stream water, suggesting that decreasing riparian vegetation density could increase fecal bacteria surface runoff.